Starting phenix.real_space_refine on Fri Mar 6 03:13:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wtd_32779/03_2026/7wtd_32779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtd_32779/03_2026/7wtd_32779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wtd_32779/03_2026/7wtd_32779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtd_32779/03_2026/7wtd_32779.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wtd_32779/03_2026/7wtd_32779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtd_32779/03_2026/7wtd_32779.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 152 5.16 5 C 17157 2.51 5 N 4733 2.21 5 O 5083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27137 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4625 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 40, 'TRANS': 559} Chain: "B" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4625 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 40, 'TRANS': 559} Chain: "C" Number of atoms: 8869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8869 Classifications: {'peptide': 1146} Link IDs: {'CIS': 1, 'PTRANS': 65, 'TRANS': 1079} Chain: "D" Number of atoms: 8860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1145, 8860 Classifications: {'peptide': 1145} Link IDs: {'PTRANS': 65, 'TRANS': 1079} Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'ATP': 1, 'COA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'ATP': 1, 'COA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.22, per 1000 atoms: 0.19 Number of scatterers: 27137 At special positions: 0 Unit cell: (159.5, 152.9, 134.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 12 15.00 O 5083 8.00 N 4733 7.00 C 17157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 786 " distance=2.03 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.02 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 786 " distance=2.03 Simple disulfide: pdb=" SG CYS D 752 " - pdb=" SG CYS D 786 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.4 seconds 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6426 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 22 sheets defined 47.2% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.890A pdb=" N LEU A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.848A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 571 through 577 Processing helix chain 'A' and resid 583 through 589 removed outlier: 3.710A pdb=" N LEU A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 598 Processing helix chain 'A' and resid 611 through 618 removed outlier: 3.744A pdb=" N MET A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 removed outlier: 3.766A pdb=" N GLU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 669 Processing helix chain 'A' and resid 682 through 697 removed outlier: 3.536A pdb=" N MET A 686 " --> pdb=" O TYR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 734 Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'A' and resid 778 through 788 Processing helix chain 'A' and resid 809 through 817 removed outlier: 3.563A pdb=" N THR A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 843 removed outlier: 3.615A pdb=" N VAL A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 867 through 882 Processing helix chain 'A' and resid 886 through 901 removed outlier: 3.982A pdb=" N VAL A 890 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 924 Processing helix chain 'A' and resid 928 through 934 removed outlier: 3.755A pdb=" N GLN A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 949 Processing helix chain 'A' and resid 960 through 969 Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.995A pdb=" N LEU A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 3.520A pdb=" N PHE A1017 " --> pdb=" O TYR A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1040 Processing helix chain 'B' and resid 496 through 510 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 571 through 578 removed outlier: 3.830A pdb=" N GLN B 575 " --> pdb=" O ARG B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 removed outlier: 3.600A pdb=" N LEU B 587 " --> pdb=" O ARG B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 Processing helix chain 'B' and resid 608 through 611 removed outlier: 3.832A pdb=" N THR B 611 " --> pdb=" O GLY B 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 608 through 611' Processing helix chain 'B' and resid 612 through 618 Processing helix chain 'B' and resid 622 through 629 removed outlier: 3.720A pdb=" N GLU B 629 " --> pdb=" O ARG B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 removed outlier: 3.603A pdb=" N VAL B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY B 670 " --> pdb=" O ALA B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 697 removed outlier: 3.630A pdb=" N MET B 686 " --> pdb=" O TYR B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 734 removed outlier: 3.543A pdb=" N TYR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 removed outlier: 4.194A pdb=" N ARG B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 790 removed outlier: 3.733A pdb=" N ALA B 782 " --> pdb=" O ALA B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 817 removed outlier: 3.700A pdb=" N LEU B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 843 removed outlier: 3.792A pdb=" N PHE B 832 " --> pdb=" O MET B 828 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 846 No H-bonds generated for 'chain 'B' and resid 844 through 846' Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 867 through 881 removed outlier: 3.838A pdb=" N ASN B 873 " --> pdb=" O GLY B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 902 removed outlier: 3.549A pdb=" N VAL B 890 " --> pdb=" O LYS B 886 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 894 " --> pdb=" O VAL B 890 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 924 removed outlier: 3.872A pdb=" N LYS B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 934 Processing helix chain 'B' and resid 941 through 950 removed outlier: 3.722A pdb=" N GLY B 950 " --> pdb=" O GLU B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 969 removed outlier: 3.909A pdb=" N ARG B 964 " --> pdb=" O PRO B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 986 through 999 removed outlier: 4.068A pdb=" N LEU B 990 " --> pdb=" O ASP B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1013 removed outlier: 3.601A pdb=" N VAL B1007 " --> pdb=" O THR B1003 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR B1013 " --> pdb=" O SER B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1028 Processing helix chain 'B' and resid 1034 through 1040 Processing helix chain 'C' and resid 46 through 59 removed outlier: 3.663A pdb=" N ILE C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 109 removed outlier: 3.548A pdb=" N ASN C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.675A pdb=" N ALA C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 149 Processing helix chain 'C' and resid 151 through 162 removed outlier: 3.848A pdb=" N ALA C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.548A pdb=" N TYR C 187 " --> pdb=" O PHE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 227 removed outlier: 3.759A pdb=" N GLU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 303 Processing helix chain 'C' and resid 332 through 341 removed outlier: 4.515A pdb=" N THR C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 354 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 435 through 450 Processing helix chain 'C' and resid 458 through 468 removed outlier: 3.621A pdb=" N LEU C 462 " --> pdb=" O ASN C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 474 removed outlier: 3.516A pdb=" N GLY C 474 " --> pdb=" O GLN C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 481 removed outlier: 4.385A pdb=" N ILE C 481 " --> pdb=" O THR C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 511 Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 549 through 559 Processing helix chain 'C' and resid 571 through 578 removed outlier: 4.397A pdb=" N GLN C 575 " --> pdb=" O ARG C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 589 removed outlier: 3.643A pdb=" N LYS C 589 " --> pdb=" O ASP C 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 586 through 589' Processing helix chain 'C' and resid 590 through 598 Processing helix chain 'C' and resid 608 through 612 removed outlier: 4.412A pdb=" N PHE C 612 " --> pdb=" O GLY C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 634 removed outlier: 4.550A pdb=" N GLU C 629 " --> pdb=" O ARG C 625 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU C 630 " --> pdb=" O ARG C 626 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU C 632 " --> pdb=" O GLN C 628 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 removed outlier: 3.526A pdb=" N VAL C 659 " --> pdb=" O PRO C 655 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 670 " --> pdb=" O ALA C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 697 removed outlier: 4.090A pdb=" N MET C 686 " --> pdb=" O TYR C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 734 removed outlier: 3.660A pdb=" N TYR C 723 " --> pdb=" O SER C 719 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY C 734 " --> pdb=" O LEU C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 removed outlier: 4.150A pdb=" N ASP C 761 " --> pdb=" O SER C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 790 Processing helix chain 'C' and resid 798 through 802 Processing helix chain 'C' and resid 809 through 817 removed outlier: 3.953A pdb=" N LEU C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 843 removed outlier: 3.577A pdb=" N ASP C 833 " --> pdb=" O GLU C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 846 No H-bonds generated for 'chain 'C' and resid 844 through 846' Processing helix chain 'C' and resid 849 through 854 Processing helix chain 'C' and resid 860 through 865 removed outlier: 3.983A pdb=" N ASN C 864 " --> pdb=" O ASP C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 881 removed outlier: 4.349A pdb=" N THR C 872 " --> pdb=" O GLY C 868 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASN C 873 " --> pdb=" O GLY C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 893 removed outlier: 3.536A pdb=" N VAL C 890 " --> pdb=" O LYS C 886 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 893 " --> pdb=" O GLU C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 901 Processing helix chain 'C' and resid 908 through 925 removed outlier: 4.255A pdb=" N LYS C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 934 removed outlier: 3.624A pdb=" N ALA C 931 " --> pdb=" O SER C 927 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 934 " --> pdb=" O GLU C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 950 removed outlier: 3.861A pdb=" N GLY C 950 " --> pdb=" O GLU C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 968 removed outlier: 3.733A pdb=" N ARG C 964 " --> pdb=" O PRO C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 987 through 998 removed outlier: 3.997A pdb=" N GLU C 991 " --> pdb=" O LEU C 987 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1013 Processing helix chain 'C' and resid 1013 through 1027 Processing helix chain 'C' and resid 1034 through 1040 Processing helix chain 'D' and resid 46 through 59 removed outlier: 3.511A pdb=" N LEU D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 124 through 134 removed outlier: 3.842A pdb=" N ALA D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 150 Processing helix chain 'D' and resid 151 through 162 removed outlier: 3.954A pdb=" N ALA D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 removed outlier: 3.596A pdb=" N TYR D 187 " --> pdb=" O PHE D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 228 removed outlier: 3.797A pdb=" N GLU D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 303 Processing helix chain 'D' and resid 332 through 340 removed outlier: 3.994A pdb=" N THR D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE D 339 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 354 Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 435 through 450 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 468 through 474 removed outlier: 3.538A pdb=" N LEU D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 481 removed outlier: 4.245A pdb=" N ILE D 481 " --> pdb=" O THR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 488 removed outlier: 3.647A pdb=" N PHE D 488 " --> pdb=" O PRO D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 510 Processing helix chain 'D' and resid 541 through 548 removed outlier: 3.652A pdb=" N LEU D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 571 through 577 removed outlier: 3.742A pdb=" N GLN D 575 " --> pdb=" O ARG D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.962A pdb=" N LEU D 587 " --> pdb=" O ARG D 583 " (cutoff:3.500A) Proline residue: D 592 - end of helix Processing helix chain 'D' and resid 608 through 617 removed outlier: 3.808A pdb=" N PHE D 612 " --> pdb=" O GLY D 608 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP D 613 " --> pdb=" O GLY D 609 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET D 616 " --> pdb=" O PHE D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 655 through 670 removed outlier: 3.546A pdb=" N GLY D 670 " --> pdb=" O ALA D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 697 Processing helix chain 'D' and resid 719 through 734 Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'D' and resid 778 through 790 removed outlier: 3.528A pdb=" N ALA D 782 " --> pdb=" O ALA D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 816 Processing helix chain 'D' and resid 827 through 843 removed outlier: 4.057A pdb=" N VAL D 831 " --> pdb=" O PRO D 827 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 848 removed outlier: 4.816A pdb=" N ALA D 847 " --> pdb=" O LEU D 844 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE D 848 " --> pdb=" O TYR D 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 844 through 848' Processing helix chain 'D' and resid 849 through 854 removed outlier: 3.852A pdb=" N THR D 853 " --> pdb=" O ASP D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 881 removed outlier: 3.605A pdb=" N THR D 872 " --> pdb=" O GLY D 868 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN D 873 " --> pdb=" O GLY D 869 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 874 " --> pdb=" O GLN D 870 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 878 " --> pdb=" O LEU D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 removed outlier: 4.093A pdb=" N VAL D 895 " --> pdb=" O LYS D 891 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 901 " --> pdb=" O ALA D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 925 Processing helix chain 'D' and resid 927 through 934 Processing helix chain 'D' and resid 941 through 950 Processing helix chain 'D' and resid 960 through 969 Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 986 through 998 removed outlier: 4.367A pdb=" N LEU D 990 " --> pdb=" O ASP D 986 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU D 991 " --> pdb=" O LEU D 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 992 " --> pdb=" O GLN D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1003 through 1013 removed outlier: 4.080A pdb=" N VAL D1007 " --> pdb=" O THR D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1028 Processing helix chain 'D' and resid 1034 through 1040 Processing sheet with id=AA1, first strand: chain 'A' and resid 639 through 640 removed outlier: 8.135A pdb=" N GLN A 640 " --> pdb=" O PHE A 602 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N MET A 604 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 565 " --> pdb=" O PHE A 602 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET A 604 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP A 567 " --> pdb=" O MET A 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 642 through 644 removed outlier: 7.020A pdb=" N VAL A 700 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N CYS A 739 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 702 " --> pdb=" O CYS A 739 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LYS A 741 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 704 " --> pdb=" O LYS A 741 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1047 through 1050 removed outlier: 3.611A pdb=" N VAL A1050 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A1058 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ALA A1062 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 564 through 567 removed outlier: 7.717A pdb=" N LEU B 565 " --> pdb=" O PHE B 602 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET B 604 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP B 567 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLN B 640 " --> pdb=" O PHE B 602 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N MET B 604 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU B 642 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 639 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ARG B 675 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET B 641 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE B 674 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 700 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS B 739 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA B 702 " --> pdb=" O CYS B 739 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS B 741 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 704 " --> pdb=" O LYS B 741 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU B 738 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N HIS B 771 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE B 740 " --> pdb=" O HIS B 771 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B 768 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASP B 795 " --> pdb=" O LEU B 768 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE B 770 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 796 " --> pdb=" O MET B 566 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1047 through 1051 removed outlier: 3.581A pdb=" N VAL B1050 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B1058 " --> pdb=" O VAL B1050 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA B1062 " --> pdb=" O GLU B1079 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU B1079 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA B1064 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B1077 " --> pdb=" O ALA B1064 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 85 removed outlier: 6.486A pdb=" N VAL C 40 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE C 66 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL C 42 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS C 39 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N HIS C 115 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N MET C 41 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 206 through 207 removed outlier: 3.771A pdb=" N GLU C 236 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 325 through 326 removed outlier: 6.323A pdb=" N GLU C 246 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU C 262 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN C 248 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER C 266 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL C 275 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN C 268 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LYS C 273 " --> pdb=" O GLN C 268 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL C 274 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG C 377 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS C 372 " --> pdb=" O HIS C 432 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N HIS C 432 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 374 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE C 430 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS C 376 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS C 428 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL C 378 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 381 through 382 removed outlier: 3.701A pdb=" N GLN C 388 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.137A pdb=" N GLY C 392 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 396 through 398 removed outlier: 4.078A pdb=" N ARG C 451 " --> pdb=" O ARG C 398 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 564 through 566 removed outlier: 6.169A pdb=" N LEU C 564 " --> pdb=" O VAL C 794 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 770 " --> pdb=" O VAL C 793 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 795 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR C 772 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 700 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N CYS C 739 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA C 702 " --> pdb=" O CYS C 739 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS C 741 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE C 704 " --> pdb=" O LYS C 741 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA C 703 " --> pdb=" O VAL C 676 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 604 through 605 removed outlier: 6.338A pdb=" N MET C 604 " --> pdb=" O GLN C 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 1047 through 1053 removed outlier: 7.336A pdb=" N GLU C1047 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ALA C1062 " --> pdb=" O GLU C1047 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU C1049 " --> pdb=" O ILE C1060 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE C1060 " --> pdb=" O GLU C1049 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLU C1051 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU C1058 " --> pdb=" O GLU C1051 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C1053 " --> pdb=" O LYS C1056 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA C1062 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLU C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C1076 " --> pdb=" O ILE C1087 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 82 through 85 removed outlier: 6.340A pdb=" N VAL D 40 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE D 66 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL D 42 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 113 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 204 through 207 removed outlier: 3.510A pdb=" N ARG D 205 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 257 through 259 removed outlier: 3.843A pdb=" N GLU D 324 " --> pdb=" O GLU D 311 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 275 through 277 removed outlier: 3.657A pdb=" N VAL D 427 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 381 through 382 removed outlier: 3.802A pdb=" N GLN D 388 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 564 through 567 removed outlier: 8.588A pdb=" N GLU D 605 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP D 567 " --> pdb=" O GLU D 605 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE D 639 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG D 675 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET D 641 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE D 677 " --> pdb=" O MET D 641 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU D 643 " --> pdb=" O PHE D 677 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 674 " --> pdb=" O VAL D 699 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL D 700 " --> pdb=" O ILE D 737 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS D 739 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA D 702 " --> pdb=" O CYS D 739 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS D 741 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE D 704 " --> pdb=" O LYS D 741 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1047 through 1051 removed outlier: 6.512A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL D1065 " --> pdb=" O GLN D1075 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN D1075 " --> pdb=" O VAL D1065 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1112 through 1114 removed outlier: 5.635A pdb=" N ALA D1114 " --> pdb=" O LEU D1173 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU D1173 " --> pdb=" O ALA D1114 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4583 1.30 - 1.44: 7057 1.44 - 1.57: 15813 1.57 - 1.70: 30 1.70 - 1.84: 262 Bond restraints: 27745 Sorted by residual: bond pdb=" C1B COA C2001 " pdb=" C2B COA C2001 " ideal model delta sigma weight residual 1.533 1.328 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C1B COA D2001 " pdb=" C2B COA D2001 " ideal model delta sigma weight residual 1.533 1.329 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C1B COA D2001 " pdb=" O4B COA D2001 " ideal model delta sigma weight residual 1.418 1.595 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" C1B COA C2001 " pdb=" O4B COA C2001 " ideal model delta sigma weight residual 1.418 1.592 -0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" C3B COA C2001 " pdb=" C4B COA C2001 " ideal model delta sigma weight residual 1.529 1.358 0.171 2.00e-02 2.50e+03 7.28e+01 ... (remaining 27740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 37453 4.18 - 8.35: 170 8.35 - 12.53: 15 12.53 - 16.71: 1 16.71 - 20.88: 7 Bond angle restraints: 37646 Sorted by residual: angle pdb=" PB ATP C2000 " pdb=" O3B ATP C2000 " pdb=" PG ATP C2000 " ideal model delta sigma weight residual 139.87 132.69 7.18 1.00e+00 1.00e+00 5.16e+01 angle pdb=" C1B COA C2001 " pdb=" N9A COA C2001 " pdb=" C8A COA C2001 " ideal model delta sigma weight residual 124.69 103.81 20.88 3.00e+00 1.11e-01 4.85e+01 angle pdb=" C1B COA D2001 " pdb=" N9A COA D2001 " pdb=" C8A COA D2001 " ideal model delta sigma weight residual 124.69 104.65 20.04 3.00e+00 1.11e-01 4.46e+01 angle pdb=" N1A COA D2001 " pdb=" C6A COA D2001 " pdb=" N6A COA D2001 " ideal model delta sigma weight residual 119.19 99.57 19.62 3.00e+00 1.11e-01 4.28e+01 angle pdb=" N1A COA C2001 " pdb=" C6A COA C2001 " pdb=" N6A COA C2001 " ideal model delta sigma weight residual 119.19 100.08 19.11 3.00e+00 1.11e-01 4.06e+01 ... (remaining 37641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 15171 18.09 - 36.19: 1315 36.19 - 54.28: 268 54.28 - 72.37: 88 72.37 - 90.47: 30 Dihedral angle restraints: 16872 sinusoidal: 6857 harmonic: 10015 Sorted by residual: dihedral pdb=" CB CYS A 752 " pdb=" SG CYS A 752 " pdb=" SG CYS A 786 " pdb=" CB CYS A 786 " ideal model delta sinusoidal sigma weight residual 93.00 -176.53 -90.47 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS B 752 " pdb=" SG CYS B 752 " pdb=" SG CYS B 786 " pdb=" CB CYS B 786 " ideal model delta sinusoidal sigma weight residual 93.00 174.82 -81.82 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CB CYS C 752 " pdb=" SG CYS C 752 " pdb=" SG CYS C 786 " pdb=" CB CYS C 786 " ideal model delta sinusoidal sigma weight residual 93.00 154.22 -61.22 1 1.00e+01 1.00e-02 4.98e+01 ... (remaining 16869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3666 0.074 - 0.147: 467 0.147 - 0.221: 26 0.221 - 0.294: 1 0.294 - 0.368: 3 Chirality restraints: 4163 Sorted by residual: chirality pdb=" CB VAL C 164 " pdb=" CA VAL C 164 " pdb=" CG1 VAL C 164 " pdb=" CG2 VAL C 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA VAL C 164 " pdb=" N VAL C 164 " pdb=" C VAL C 164 " pdb=" CB VAL C 164 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C3B COA C2001 " pdb=" C2B COA C2001 " pdb=" C4B COA C2001 " pdb=" O3B COA C2001 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 4160 not shown) Planarity restraints: 4950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 199 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C GLY C 199 " 0.074 2.00e-02 2.50e+03 pdb=" O GLY C 199 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY C 200 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D1030 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C LEU D1030 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU D1030 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP D1031 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 908 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO C 909 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 909 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 909 " 0.037 5.00e-02 4.00e+02 ... (remaining 4947 not shown) Histogram of nonbonded interaction distances: 0.99 - 1.77: 6 1.77 - 2.55: 344 2.55 - 3.34: 35186 3.34 - 4.12: 66127 4.12 - 4.90: 116215 Warning: very small nonbonded interaction distances. Nonbonded interactions: 217878 Sorted by model distance: nonbonded pdb=" NH2 ARG C 393 " pdb=" OE1 GLN C1075 " model vdw 0.990 3.120 nonbonded pdb=" OE2 GLU C 395 " pdb=" N LEU C1088 " model vdw 1.323 3.120 nonbonded pdb=" NE2 GLN C 78 " pdb=" OD1 ASN D1081 " model vdw 1.374 3.120 nonbonded pdb=" OE1 GLN D 388 " pdb=" CE MET D1145 " model vdw 1.463 3.460 nonbonded pdb=" O ASN C1081 " pdb=" OE1 GLN D 78 " model vdw 1.580 3.040 ... (remaining 217873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 34 through 1178) selection = (chain 'D' and resid 34 through 1178) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.340 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.825 27755 Z= 0.653 Angle : 0.841 20.884 37654 Z= 0.442 Chirality : 0.047 0.368 4163 Planarity : 0.005 0.071 4950 Dihedral : 14.981 89.743 10434 Min Nonbonded Distance : 0.990 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 1.15 % Allowed : 0.87 % Favored : 97.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3483 helix: 0.63 (0.14), residues: 1407 sheet: -0.40 (0.24), residues: 471 loop : -1.77 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 219 TYR 0.023 0.002 TYR D 304 PHE 0.028 0.001 PHE A 876 TRP 0.042 0.003 TRP C 624 HIS 0.019 0.001 HIS C 998 Details of bonding type rmsd covalent geometry : bond 0.00548 (27745) covalent geometry : angle 0.83999 (37646) SS BOND : bond 0.00455 ( 4) SS BOND : angle 2.70188 ( 8) hydrogen bonds : bond 0.19062 ( 1095) hydrogen bonds : angle 7.18956 ( 3210) Misc. bond : bond 0.39493 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 502 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 LYS cc_start: 0.7347 (mttt) cc_final: 0.6916 (mttt) REVERT: A 641 MET cc_start: 0.6574 (ptp) cc_final: 0.6223 (ptt) REVERT: A 675 ARG cc_start: 0.6946 (ttm170) cc_final: 0.6222 (mtt-85) REVERT: A 686 MET cc_start: 0.9322 (mpp) cc_final: 0.9116 (mpp) REVERT: A 828 MET cc_start: 0.8521 (ttt) cc_final: 0.8279 (tpp) REVERT: A 986 ASP cc_start: 0.8679 (t0) cc_final: 0.8334 (t0) REVERT: A 992 LYS cc_start: 0.7461 (mmpt) cc_final: 0.7073 (mmtt) REVERT: B 504 LEU cc_start: 0.9080 (mm) cc_final: 0.8703 (pp) REVERT: B 724 MET cc_start: 0.9310 (mpp) cc_final: 0.8960 (mpp) REVERT: C 92 PRO cc_start: 0.9037 (Cg_exo) cc_final: 0.8679 (Cg_endo) REVERT: C 204 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.5895 (mtt) REVERT: C 492 PRO cc_start: 0.7413 (Cg_endo) cc_final: 0.6527 (Cg_exo) REVERT: C 496 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7323 (mpp80) REVERT: C 502 HIS cc_start: 0.9031 (m90) cc_final: 0.8655 (m90) REVERT: C 686 MET cc_start: 0.8730 (mpp) cc_final: 0.7637 (mpp) REVERT: C 724 MET cc_start: 0.8872 (mmm) cc_final: 0.8449 (mmm) REVERT: C 754 MET cc_start: 0.9458 (pmm) cc_final: 0.9118 (pmm) REVERT: C 801 MET cc_start: 0.8127 (mpp) cc_final: 0.7721 (mpp) REVERT: C 854 MET cc_start: 0.7831 (mmm) cc_final: 0.7413 (mpp) REVERT: C 1032 SER cc_start: 0.8337 (m) cc_final: 0.8125 (t) REVERT: C 1038 PHE cc_start: 0.8563 (t80) cc_final: 0.8222 (t80) REVERT: C 1048 PHE cc_start: 0.8758 (p90) cc_final: 0.8484 (p90) REVERT: C 1098 MET cc_start: 0.7406 (tmm) cc_final: 0.7173 (tpp) REVERT: D 453 ARG cc_start: 0.4412 (OUTLIER) cc_final: 0.2005 (mmt180) REVERT: D 500 LEU cc_start: 0.9269 (mt) cc_final: 0.9055 (mm) REVERT: D 604 MET cc_start: 0.7219 (tpt) cc_final: 0.6670 (tpp) REVERT: D 641 MET cc_start: 0.6989 (ptm) cc_final: 0.5257 (tmm) REVERT: D 671 MET cc_start: 0.3811 (tpt) cc_final: 0.2996 (tpt) REVERT: D 784 LEU cc_start: 0.9233 (mm) cc_final: 0.8892 (pp) REVERT: D 920 PHE cc_start: 0.7319 (t80) cc_final: 0.7081 (t80) REVERT: D 1116 MET cc_start: 0.4981 (mpp) cc_final: 0.4673 (ptm) REVERT: D 1122 ASP cc_start: 0.8629 (m-30) cc_final: 0.8289 (p0) REVERT: D 1145 MET cc_start: 0.4614 (mtm) cc_final: 0.3340 (ttm) outliers start: 33 outliers final: 3 residues processed: 524 average time/residue: 0.1893 time to fit residues: 151.5965 Evaluate side-chains 309 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 303 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain D residue 453 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.0040 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN A1075 GLN ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 HIS C 44 ASN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN C 506 HIS C 773 HIS C 898 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS D 463 GLN D 467 ASN D 494 GLN ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.074913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.060707 restraints weight = 201933.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.062404 restraints weight = 130145.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.063619 restraints weight = 93475.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.064437 restraints weight = 72438.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.065078 restraints weight = 59820.839| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27755 Z= 0.163 Angle : 0.723 12.051 37654 Z= 0.367 Chirality : 0.047 0.284 4163 Planarity : 0.005 0.069 4950 Dihedral : 8.712 87.339 3992 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.89 % Favored : 93.08 % Rotamer: Outliers : 1.99 % Allowed : 11.36 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3483 helix: 0.49 (0.13), residues: 1449 sheet: -0.47 (0.24), residues: 461 loop : -1.79 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 54 TYR 0.025 0.002 TYR B1013 PHE 0.028 0.002 PHE A 876 TRP 0.028 0.002 TRP A 607 HIS 0.016 0.002 HIS C 574 Details of bonding type rmsd covalent geometry : bond 0.00346 (27745) covalent geometry : angle 0.72258 (37646) SS BOND : bond 0.00447 ( 4) SS BOND : angle 1.92344 ( 8) hydrogen bonds : bond 0.04590 ( 1095) hydrogen bonds : angle 5.82240 ( 3210) Misc. bond : bond 0.00642 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 324 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9199 (tp) cc_final: 0.8973 (pt) REVERT: A 566 MET cc_start: 0.6903 (ttp) cc_final: 0.5544 (ttp) REVERT: A 577 LEU cc_start: 0.8706 (tp) cc_final: 0.8391 (tp) REVERT: A 583 ARG cc_start: 0.8340 (ttt180) cc_final: 0.7867 (ttm-80) REVERT: A 641 MET cc_start: 0.6838 (ptp) cc_final: 0.6235 (ptt) REVERT: A 675 ARG cc_start: 0.7498 (ttm170) cc_final: 0.6693 (mtm180) REVERT: A 686 MET cc_start: 0.9200 (mpp) cc_final: 0.8977 (mpp) REVERT: A 724 MET cc_start: 0.8485 (tpp) cc_final: 0.8146 (tpt) REVERT: A 743 MET cc_start: 0.7547 (tpt) cc_final: 0.7067 (tpp) REVERT: A 986 ASP cc_start: 0.8691 (t0) cc_final: 0.8292 (t0) REVERT: A 1077 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: B 724 MET cc_start: 0.9436 (mpp) cc_final: 0.9087 (mpp) REVERT: B 828 MET cc_start: 0.8161 (ppp) cc_final: 0.7770 (ppp) REVERT: C 75 MET cc_start: 0.6451 (ptp) cc_final: 0.6251 (ptp) REVERT: C 204 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7316 (mmp) REVERT: C 300 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6938 (pptt) REVERT: C 422 TYR cc_start: 0.4040 (m-80) cc_final: 0.3481 (m-80) REVERT: C 464 ASN cc_start: 0.8971 (t0) cc_final: 0.8763 (t0) REVERT: C 502 HIS cc_start: 0.9106 (m90) cc_final: 0.8906 (m90) REVERT: C 604 MET cc_start: 0.8533 (mmm) cc_final: 0.7654 (tpp) REVERT: C 686 MET cc_start: 0.8712 (mpp) cc_final: 0.7825 (mpp) REVERT: C 724 MET cc_start: 0.9090 (mmm) cc_final: 0.8660 (mmm) REVERT: C 854 MET cc_start: 0.7799 (mmm) cc_final: 0.7534 (mpp) REVERT: C 874 LEU cc_start: 0.9077 (tp) cc_final: 0.8674 (mt) REVERT: C 1032 SER cc_start: 0.8777 (m) cc_final: 0.8399 (t) REVERT: C 1038 PHE cc_start: 0.8756 (t80) cc_final: 0.8336 (t80) REVERT: C 1048 PHE cc_start: 0.9105 (p90) cc_final: 0.8752 (p90) REVERT: C 1075 GLN cc_start: 0.8591 (tt0) cc_final: 0.8367 (tt0) REVERT: D 71 ASP cc_start: 0.6652 (t0) cc_final: 0.6439 (t0) REVERT: D 74 GLN cc_start: 0.8168 (tp40) cc_final: 0.7866 (tp40) REVERT: D 239 ILE cc_start: 0.2339 (mp) cc_final: 0.2026 (mm) REVERT: D 353 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6912 (mm-30) REVERT: D 443 MET cc_start: 0.9284 (tpt) cc_final: 0.8941 (tpt) REVERT: D 453 ARG cc_start: 0.4642 (OUTLIER) cc_final: 0.3757 (mmm-85) REVERT: D 500 LEU cc_start: 0.9281 (mt) cc_final: 0.9024 (mm) REVERT: D 604 MET cc_start: 0.7243 (tpt) cc_final: 0.6674 (tpp) REVERT: D 641 MET cc_start: 0.7116 (ptm) cc_final: 0.5619 (tmm) REVERT: D 671 MET cc_start: 0.3977 (tpt) cc_final: 0.3407 (tpt) REVERT: D 686 MET cc_start: 0.8566 (mmt) cc_final: 0.8345 (mmt) REVERT: D 687 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9460 (pp) REVERT: D 728 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8756 (pt0) REVERT: D 743 MET cc_start: 0.7534 (mmp) cc_final: 0.7291 (mmm) REVERT: D 784 LEU cc_start: 0.9164 (mm) cc_final: 0.8839 (pp) REVERT: D 920 PHE cc_start: 0.7679 (t80) cc_final: 0.7289 (t80) REVERT: D 1012 MET cc_start: 0.8729 (mpp) cc_final: 0.8489 (mpp) REVERT: D 1116 MET cc_start: 0.6691 (mpp) cc_final: 0.5976 (ptp) REVERT: D 1122 ASP cc_start: 0.8633 (m-30) cc_final: 0.8281 (p0) REVERT: D 1143 MET cc_start: 0.1355 (mmp) cc_final: 0.0142 (mmm) REVERT: D 1145 MET cc_start: 0.1319 (mtm) cc_final: -0.0330 (ttp) REVERT: D 1166 MET cc_start: 0.6583 (tmm) cc_final: 0.5974 (ppp) outliers start: 57 outliers final: 25 residues processed: 362 average time/residue: 0.1658 time to fit residues: 96.4039 Evaluate side-chains 310 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 1077 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 76 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 267 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 291 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 HIS ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS C 464 ASN ** C 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1059 HIS D 44 ASN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN D 575 GLN D1075 GLN ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.070169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.056654 restraints weight = 213784.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.058091 restraints weight = 139643.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.059180 restraints weight = 101258.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.059914 restraints weight = 79471.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.060559 restraints weight = 66281.671| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27755 Z= 0.197 Angle : 0.705 10.802 37654 Z= 0.365 Chirality : 0.046 0.203 4163 Planarity : 0.005 0.096 4950 Dihedral : 8.388 88.317 3984 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.55 % Favored : 92.42 % Rotamer: Outliers : 2.82 % Allowed : 13.91 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3483 helix: 0.39 (0.13), residues: 1440 sheet: -0.68 (0.24), residues: 471 loop : -1.74 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 45 TYR 0.021 0.002 TYR C 118 PHE 0.033 0.002 PHE B1077 TRP 0.045 0.003 TRP A 607 HIS 0.017 0.002 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00425 (27745) covalent geometry : angle 0.70426 (37646) SS BOND : bond 0.00443 ( 4) SS BOND : angle 1.93535 ( 8) hydrogen bonds : bond 0.04297 ( 1095) hydrogen bonds : angle 5.68527 ( 3210) Misc. bond : bond 0.00222 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 284 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9195 (tp) cc_final: 0.8929 (pt) REVERT: A 566 MET cc_start: 0.6900 (ttp) cc_final: 0.5231 (ttp) REVERT: A 583 ARG cc_start: 0.8538 (ttt180) cc_final: 0.7947 (ttt180) REVERT: A 641 MET cc_start: 0.7237 (ptp) cc_final: 0.6931 (ptm) REVERT: A 675 ARG cc_start: 0.7720 (ttm170) cc_final: 0.6928 (mtm180) REVERT: A 686 MET cc_start: 0.9189 (mpp) cc_final: 0.8971 (mpp) REVERT: A 743 MET cc_start: 0.7488 (tpt) cc_final: 0.7227 (tpp) REVERT: A 986 ASP cc_start: 0.8703 (t0) cc_final: 0.8338 (t0) REVERT: B 496 ARG cc_start: 0.8721 (mtt180) cc_final: 0.8197 (mmm160) REVERT: B 604 MET cc_start: 0.6651 (tpt) cc_final: 0.6069 (tpp) REVERT: C 84 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6563 (m-80) REVERT: C 204 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7371 (mmp) REVERT: C 300 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6967 (pptt) REVERT: C 464 ASN cc_start: 0.9118 (t160) cc_final: 0.8910 (t0) REVERT: C 491 ARG cc_start: 0.9230 (ppt170) cc_final: 0.8871 (ptm-80) REVERT: C 502 HIS cc_start: 0.9123 (m90) cc_final: 0.8880 (m90) REVERT: C 686 MET cc_start: 0.8839 (mpp) cc_final: 0.7870 (mpp) REVERT: C 724 MET cc_start: 0.9069 (mmm) cc_final: 0.8614 (mmm) REVERT: C 828 MET cc_start: 0.8888 (ppp) cc_final: 0.8664 (ppp) REVERT: C 1038 PHE cc_start: 0.8848 (t80) cc_final: 0.8448 (t80) REVERT: C 1048 PHE cc_start: 0.9177 (p90) cc_final: 0.8920 (p90) REVERT: D 71 ASP cc_start: 0.6786 (t0) cc_final: 0.6567 (t0) REVERT: D 74 GLN cc_start: 0.8417 (tp40) cc_final: 0.8215 (tp40) REVERT: D 353 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7097 (mm-30) REVERT: D 374 ILE cc_start: 0.8915 (mm) cc_final: 0.8564 (pt) REVERT: D 500 LEU cc_start: 0.9308 (mt) cc_final: 0.9001 (mm) REVERT: D 604 MET cc_start: 0.7336 (tpt) cc_final: 0.6551 (tpp) REVERT: D 641 MET cc_start: 0.7354 (ptm) cc_final: 0.5682 (ppp) REVERT: D 671 MET cc_start: 0.4712 (tpt) cc_final: 0.4483 (tpt) REVERT: D 686 MET cc_start: 0.8602 (mmt) cc_final: 0.8352 (mmt) REVERT: D 743 MET cc_start: 0.7738 (mmp) cc_final: 0.7530 (mmm) REVERT: D 784 LEU cc_start: 0.9107 (mm) cc_final: 0.8730 (pp) REVERT: D 920 PHE cc_start: 0.7781 (t80) cc_final: 0.7405 (t80) REVERT: D 1116 MET cc_start: 0.6658 (mpp) cc_final: 0.6136 (ptp) REVERT: D 1122 ASP cc_start: 0.8668 (m-30) cc_final: 0.8305 (p0) REVERT: D 1143 MET cc_start: 0.1431 (mmp) cc_final: 0.0046 (mmm) REVERT: D 1166 MET cc_start: 0.6227 (tmm) cc_final: 0.5285 (ppp) outliers start: 81 outliers final: 44 residues processed: 337 average time/residue: 0.1569 time to fit residues: 86.7885 Evaluate side-chains 315 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 268 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1084 LEU Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 345 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 308 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 ASN B 574 HIS ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 432 HIS ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.068256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.054971 restraints weight = 215791.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.056384 restraints weight = 140333.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.057352 restraints weight = 102485.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.058106 restraints weight = 80854.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.058735 restraints weight = 67270.655| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27755 Z= 0.181 Angle : 0.690 10.797 37654 Z= 0.355 Chirality : 0.045 0.189 4163 Planarity : 0.005 0.055 4950 Dihedral : 8.203 86.835 3984 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.76 % Rotamer: Outliers : 2.96 % Allowed : 16.00 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3483 helix: 0.32 (0.13), residues: 1461 sheet: -0.89 (0.23), residues: 495 loop : -1.69 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 54 TYR 0.031 0.002 TYR B1013 PHE 0.039 0.002 PHE A1017 TRP 0.022 0.002 TRP A 607 HIS 0.050 0.002 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.00389 (27745) covalent geometry : angle 0.68973 (37646) SS BOND : bond 0.00450 ( 4) SS BOND : angle 2.22588 ( 8) hydrogen bonds : bond 0.03964 ( 1095) hydrogen bonds : angle 5.57911 ( 3210) Misc. bond : bond 0.00089 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 274 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9275 (tp) cc_final: 0.8999 (pt) REVERT: A 566 MET cc_start: 0.6832 (ttp) cc_final: 0.5020 (ttp) REVERT: A 583 ARG cc_start: 0.8709 (ttt180) cc_final: 0.8396 (ttm170) REVERT: A 641 MET cc_start: 0.7341 (ptp) cc_final: 0.7061 (ptm) REVERT: A 675 ARG cc_start: 0.7898 (ttm170) cc_final: 0.7013 (mtm180) REVERT: A 681 ASN cc_start: 0.7243 (p0) cc_final: 0.7028 (p0) REVERT: A 743 MET cc_start: 0.7495 (tpt) cc_final: 0.7289 (tpp) REVERT: A 986 ASP cc_start: 0.8622 (t0) cc_final: 0.8284 (t0) REVERT: A 1075 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: B 496 ARG cc_start: 0.8721 (mtt180) cc_final: 0.8201 (mmm160) REVERT: B 604 MET cc_start: 0.6938 (tpt) cc_final: 0.6568 (tpp) REVERT: B 754 MET cc_start: 0.9217 (mmm) cc_final: 0.8933 (mmm) REVERT: C 204 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7395 (mmp) REVERT: C 300 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6994 (pptt) REVERT: C 403 MET cc_start: 0.5923 (tmt) cc_final: 0.5706 (tmt) REVERT: C 442 LYS cc_start: 0.9364 (mttt) cc_final: 0.9045 (mttt) REVERT: C 464 ASN cc_start: 0.9083 (t0) cc_final: 0.8869 (t0) REVERT: C 491 ARG cc_start: 0.9192 (ppt170) cc_final: 0.8785 (ptm-80) REVERT: C 583 ARG cc_start: 0.8621 (ttt-90) cc_final: 0.8232 (mtp180) REVERT: C 604 MET cc_start: 0.8596 (mmm) cc_final: 0.7782 (tpp) REVERT: C 686 MET cc_start: 0.8862 (mpp) cc_final: 0.8011 (mpp) REVERT: C 724 MET cc_start: 0.9129 (mmm) cc_final: 0.8682 (mmm) REVERT: C 828 MET cc_start: 0.8983 (ppp) cc_final: 0.8746 (ppp) REVERT: C 1038 PHE cc_start: 0.8842 (t80) cc_final: 0.8619 (t80) REVERT: C 1048 PHE cc_start: 0.9187 (p90) cc_final: 0.8910 (p90) REVERT: D 38 LYS cc_start: 0.8188 (pttm) cc_final: 0.7925 (pttm) REVERT: D 74 GLN cc_start: 0.8544 (tp40) cc_final: 0.8235 (mp10) REVERT: D 294 ASP cc_start: 0.8218 (m-30) cc_final: 0.7877 (t0) REVERT: D 374 ILE cc_start: 0.8887 (mm) cc_final: 0.8556 (pt) REVERT: D 500 LEU cc_start: 0.9333 (mt) cc_final: 0.9020 (mm) REVERT: D 508 MET cc_start: 0.9195 (ptp) cc_final: 0.8987 (ptp) REVERT: D 641 MET cc_start: 0.7402 (ptm) cc_final: 0.5685 (ppp) REVERT: D 671 MET cc_start: 0.5113 (tpt) cc_final: 0.4880 (tpt) REVERT: D 743 MET cc_start: 0.7592 (mmp) cc_final: 0.7359 (mmm) REVERT: D 784 LEU cc_start: 0.9058 (mm) cc_final: 0.8673 (pp) REVERT: D 804 MET cc_start: 0.8654 (mmp) cc_final: 0.8310 (mmp) REVERT: D 854 MET cc_start: 0.8704 (mmp) cc_final: 0.8182 (tpp) REVERT: D 920 PHE cc_start: 0.7885 (t80) cc_final: 0.7394 (t80) REVERT: D 1116 MET cc_start: 0.6440 (mpp) cc_final: 0.6051 (ptp) REVERT: D 1122 ASP cc_start: 0.8691 (m-30) cc_final: 0.8369 (p0) REVERT: D 1143 MET cc_start: 0.1780 (mmp) cc_final: 0.0337 (mmm) REVERT: D 1166 MET cc_start: 0.6212 (tmm) cc_final: 0.5191 (ppp) outliers start: 85 outliers final: 47 residues processed: 333 average time/residue: 0.1610 time to fit residues: 87.0030 Evaluate side-chains 305 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1075 GLN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 179 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 282 optimal weight: 0.0270 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 773 HIS ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS C 181 HIS C 506 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN D 467 ASN ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.068059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.054692 restraints weight = 219347.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.056103 restraints weight = 143779.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.057072 restraints weight = 104959.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.057887 restraints weight = 83244.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.058399 restraints weight = 68991.391| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 27755 Z= 0.145 Angle : 0.660 11.706 37654 Z= 0.333 Chirality : 0.044 0.174 4163 Planarity : 0.005 0.055 4950 Dihedral : 8.035 89.984 3982 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.24 % Favored : 92.74 % Rotamer: Outliers : 2.93 % Allowed : 18.02 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3483 helix: 0.44 (0.13), residues: 1462 sheet: -0.72 (0.23), residues: 486 loop : -1.71 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 453 TYR 0.022 0.002 TYR B1013 PHE 0.031 0.002 PHE A1017 TRP 0.015 0.001 TRP A 607 HIS 0.021 0.002 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00321 (27745) covalent geometry : angle 0.65939 (37646) SS BOND : bond 0.00310 ( 4) SS BOND : angle 2.23110 ( 8) hydrogen bonds : bond 0.03606 ( 1095) hydrogen bonds : angle 5.43472 ( 3210) Misc. bond : bond 0.00136 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 264 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9306 (tp) cc_final: 0.8986 (pt) REVERT: A 566 MET cc_start: 0.6810 (ttp) cc_final: 0.4667 (ttm) REVERT: A 583 ARG cc_start: 0.8761 (ttt180) cc_final: 0.7833 (ttt180) REVERT: A 636 ASN cc_start: 0.7176 (t0) cc_final: 0.6714 (p0) REVERT: A 675 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7070 (mtt180) REVERT: A 986 ASP cc_start: 0.8625 (t0) cc_final: 0.8274 (t0) REVERT: A 1044 ILE cc_start: 0.8820 (mm) cc_final: 0.8524 (tp) REVERT: A 1075 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8186 (tm130) REVERT: B 496 ARG cc_start: 0.8677 (mtt180) cc_final: 0.8167 (mmm160) REVERT: B 604 MET cc_start: 0.7085 (tpt) cc_final: 0.6567 (tpt) REVERT: B 754 MET cc_start: 0.9237 (mmm) cc_final: 0.8918 (mmm) REVERT: C 70 GLN cc_start: 0.8559 (pm20) cc_final: 0.8347 (pm20) REVERT: C 204 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7275 (mmp) REVERT: C 300 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6959 (pptt) REVERT: C 403 MET cc_start: 0.5881 (tmt) cc_final: 0.5650 (tmt) REVERT: C 464 ASN cc_start: 0.9063 (t0) cc_final: 0.8833 (t0) REVERT: C 491 ARG cc_start: 0.9200 (ppt170) cc_final: 0.8370 (ptm-80) REVERT: C 604 MET cc_start: 0.8507 (mmm) cc_final: 0.7969 (tpp) REVERT: C 686 MET cc_start: 0.8705 (mpp) cc_final: 0.7968 (mpp) REVERT: C 724 MET cc_start: 0.9113 (mmm) cc_final: 0.8658 (mmm) REVERT: C 828 MET cc_start: 0.8981 (ppp) cc_final: 0.8695 (ppp) REVERT: C 1038 PHE cc_start: 0.8855 (t80) cc_final: 0.8561 (t80) REVERT: C 1048 PHE cc_start: 0.9166 (p90) cc_final: 0.8929 (p90) REVERT: D 74 GLN cc_start: 0.8631 (tp40) cc_final: 0.8269 (tp-100) REVERT: D 294 ASP cc_start: 0.8191 (m-30) cc_final: 0.7939 (t0) REVERT: D 374 ILE cc_start: 0.8903 (mm) cc_final: 0.8539 (pt) REVERT: D 641 MET cc_start: 0.7376 (ptm) cc_final: 0.5663 (ppp) REVERT: D 686 MET cc_start: 0.8405 (mmt) cc_final: 0.8120 (mmt) REVERT: D 724 MET cc_start: 0.8903 (mmm) cc_final: 0.8442 (mmm) REVERT: D 728 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8627 (mp0) REVERT: D 743 MET cc_start: 0.7584 (mmp) cc_final: 0.7330 (mmm) REVERT: D 784 LEU cc_start: 0.9046 (mm) cc_final: 0.8659 (pp) REVERT: D 804 MET cc_start: 0.8656 (mmp) cc_final: 0.8290 (mmp) REVERT: D 854 MET cc_start: 0.8724 (mmp) cc_final: 0.8229 (tpp) REVERT: D 920 PHE cc_start: 0.7938 (t80) cc_final: 0.7710 (t80) REVERT: D 1116 MET cc_start: 0.6422 (mpp) cc_final: 0.6099 (ptp) REVERT: D 1122 ASP cc_start: 0.8660 (m-30) cc_final: 0.8380 (p0) REVERT: D 1143 MET cc_start: 0.1899 (mmp) cc_final: 0.0302 (mmm) REVERT: D 1166 MET cc_start: 0.6326 (tmm) cc_final: 0.5440 (ppp) outliers start: 84 outliers final: 55 residues processed: 323 average time/residue: 0.1538 time to fit residues: 81.6775 Evaluate side-chains 306 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1075 GLN Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 286 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 23 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 239 optimal weight: 20.0000 chunk 315 optimal weight: 10.0000 chunk 229 optimal weight: 30.0000 chunk 187 optimal weight: 0.0980 overall best weight: 2.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS C 350 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN C 506 HIS C1040 GLN C1075 GLN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 HIS ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.067767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.054521 restraints weight = 215894.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.055957 restraints weight = 140919.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.056981 restraints weight = 102771.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.057661 restraints weight = 80551.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.058264 restraints weight = 67378.407| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 27755 Z= 0.138 Angle : 0.663 15.375 37654 Z= 0.331 Chirality : 0.044 0.271 4163 Planarity : 0.005 0.063 4950 Dihedral : 7.920 86.898 3982 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.76 % Rotamer: Outliers : 3.10 % Allowed : 18.89 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3483 helix: 0.53 (0.14), residues: 1458 sheet: -0.71 (0.23), residues: 483 loop : -1.72 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 45 TYR 0.026 0.002 TYR B 593 PHE 0.028 0.002 PHE A1017 TRP 0.013 0.001 TRP C 838 HIS 0.017 0.001 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00306 (27745) covalent geometry : angle 0.66266 (37646) SS BOND : bond 0.00284 ( 4) SS BOND : angle 2.01340 ( 8) hydrogen bonds : bond 0.03517 ( 1095) hydrogen bonds : angle 5.32558 ( 3210) Misc. bond : bond 0.00078 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 261 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9245 (tp) cc_final: 0.8994 (pt) REVERT: A 566 MET cc_start: 0.6696 (ttp) cc_final: 0.4684 (ttp) REVERT: A 583 ARG cc_start: 0.8818 (ttt180) cc_final: 0.7846 (ttt180) REVERT: A 675 ARG cc_start: 0.7978 (ttm170) cc_final: 0.6968 (mtm180) REVERT: A 986 ASP cc_start: 0.8688 (t0) cc_final: 0.8314 (t0) REVERT: A 1075 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: B 496 ARG cc_start: 0.8681 (mtt180) cc_final: 0.8182 (mmm160) REVERT: B 604 MET cc_start: 0.7190 (tpt) cc_final: 0.6677 (tpt) REVERT: B 754 MET cc_start: 0.9282 (mmm) cc_final: 0.8962 (mmm) REVERT: C 70 GLN cc_start: 0.8461 (pm20) cc_final: 0.8242 (pm20) REVERT: C 204 MET cc_start: 0.7527 (tpt) cc_final: 0.7263 (mmp) REVERT: C 300 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.7038 (pptt) REVERT: C 403 MET cc_start: 0.5762 (tmt) cc_final: 0.5535 (tmt) REVERT: C 464 ASN cc_start: 0.9127 (t0) cc_final: 0.8853 (t0) REVERT: C 491 ARG cc_start: 0.9231 (ppt170) cc_final: 0.8439 (ptm-80) REVERT: C 604 MET cc_start: 0.8506 (mmm) cc_final: 0.7995 (tpp) REVERT: C 724 MET cc_start: 0.9115 (mmm) cc_final: 0.8639 (mmm) REVERT: C 828 MET cc_start: 0.9023 (ppp) cc_final: 0.8678 (ppp) REVERT: C 881 MET cc_start: 0.8920 (mpp) cc_final: 0.8715 (mpp) REVERT: C 1038 PHE cc_start: 0.8843 (t80) cc_final: 0.8585 (t80) REVERT: C 1048 PHE cc_start: 0.9153 (p90) cc_final: 0.8907 (p90) REVERT: D 38 LYS cc_start: 0.8258 (pttm) cc_final: 0.8022 (pttm) REVERT: D 74 GLN cc_start: 0.8515 (tp40) cc_final: 0.8167 (tp-100) REVERT: D 326 ASN cc_start: 0.8329 (m-40) cc_final: 0.7343 (t0) REVERT: D 374 ILE cc_start: 0.8906 (mm) cc_final: 0.8534 (tp) REVERT: D 500 LEU cc_start: 0.9374 (mt) cc_final: 0.9172 (mm) REVERT: D 604 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8110 (mmm) REVERT: D 686 MET cc_start: 0.8483 (mmt) cc_final: 0.8128 (mmt) REVERT: D 743 MET cc_start: 0.7334 (mmp) cc_final: 0.7062 (mmm) REVERT: D 784 LEU cc_start: 0.9028 (mm) cc_final: 0.8622 (pp) REVERT: D 804 MET cc_start: 0.8593 (mmp) cc_final: 0.8209 (mmp) REVERT: D 848 PHE cc_start: 0.6479 (OUTLIER) cc_final: 0.5471 (p90) REVERT: D 854 MET cc_start: 0.8797 (mmp) cc_final: 0.8351 (tpp) REVERT: D 920 PHE cc_start: 0.8022 (t80) cc_final: 0.7790 (t80) REVERT: D 1116 MET cc_start: 0.6424 (mpp) cc_final: 0.5976 (ptp) REVERT: D 1122 ASP cc_start: 0.8688 (m-30) cc_final: 0.8403 (p0) REVERT: D 1143 MET cc_start: 0.1986 (mmp) cc_final: 0.0460 (mmm) REVERT: D 1166 MET cc_start: 0.6177 (tmm) cc_final: 0.5230 (ppp) outliers start: 89 outliers final: 68 residues processed: 324 average time/residue: 0.1677 time to fit residues: 88.5748 Evaluate side-chains 324 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 252 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1075 GLN Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 436 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1068 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 316 ARG Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1044 ILE Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 70 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 309 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 240 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.067636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.054466 restraints weight = 214580.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.055809 restraints weight = 140468.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.056853 restraints weight = 103513.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.057557 restraints weight = 81158.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.058104 restraints weight = 67592.160| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 27755 Z= 0.131 Angle : 0.673 12.931 37654 Z= 0.333 Chirality : 0.044 0.185 4163 Planarity : 0.005 0.097 4950 Dihedral : 7.713 87.218 3975 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.14 % Allowed : 19.17 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 3483 helix: 0.51 (0.14), residues: 1465 sheet: -0.61 (0.24), residues: 475 loop : -1.69 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 393 TYR 0.019 0.002 TYR A 620 PHE 0.028 0.002 PHE A1017 TRP 0.011 0.001 TRP A 624 HIS 0.014 0.001 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00298 (27745) covalent geometry : angle 0.67230 (37646) SS BOND : bond 0.00263 ( 4) SS BOND : angle 2.00265 ( 8) hydrogen bonds : bond 0.03414 ( 1095) hydrogen bonds : angle 5.30632 ( 3210) Misc. bond : bond 0.00084 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 259 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9231 (tp) cc_final: 0.8989 (pt) REVERT: A 566 MET cc_start: 0.6687 (ttp) cc_final: 0.4715 (ttp) REVERT: A 583 ARG cc_start: 0.8759 (ttt180) cc_final: 0.7814 (ttt180) REVERT: A 636 ASN cc_start: 0.7090 (t0) cc_final: 0.6682 (p0) REVERT: A 675 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7048 (mtm180) REVERT: A 986 ASP cc_start: 0.8702 (t0) cc_final: 0.8338 (t0) REVERT: A 1075 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: B 496 ARG cc_start: 0.8589 (mtt180) cc_final: 0.8115 (mmm160) REVERT: B 604 MET cc_start: 0.7156 (tpt) cc_final: 0.6853 (tpt) REVERT: B 754 MET cc_start: 0.9322 (mmm) cc_final: 0.8985 (mmm) REVERT: C 70 GLN cc_start: 0.8425 (pm20) cc_final: 0.8183 (pm20) REVERT: C 204 MET cc_start: 0.7600 (tpt) cc_final: 0.7279 (mmp) REVERT: C 300 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7041 (pptt) REVERT: C 403 MET cc_start: 0.5868 (tmt) cc_final: 0.5647 (tmt) REVERT: C 464 ASN cc_start: 0.9193 (t0) cc_final: 0.8905 (t0) REVERT: C 491 ARG cc_start: 0.9219 (ppt170) cc_final: 0.8430 (ptm-80) REVERT: C 604 MET cc_start: 0.8547 (mmm) cc_final: 0.7939 (tpp) REVERT: C 724 MET cc_start: 0.9092 (mmm) cc_final: 0.8616 (mmm) REVERT: C 1038 PHE cc_start: 0.8854 (t80) cc_final: 0.8604 (t80) REVERT: C 1048 PHE cc_start: 0.9127 (p90) cc_final: 0.8888 (p90) REVERT: D 38 LYS cc_start: 0.8291 (pttm) cc_final: 0.8050 (pttm) REVERT: D 74 GLN cc_start: 0.8666 (tp40) cc_final: 0.8283 (tp-100) REVERT: D 326 ASN cc_start: 0.8345 (m-40) cc_final: 0.7367 (t0) REVERT: D 374 ILE cc_start: 0.8907 (mm) cc_final: 0.8545 (tp) REVERT: D 500 LEU cc_start: 0.9395 (mt) cc_final: 0.9114 (mm) REVERT: D 604 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8182 (mmm) REVERT: D 641 MET cc_start: 0.6836 (ptm) cc_final: 0.5998 (ppp) REVERT: D 671 MET cc_start: 0.4194 (tpt) cc_final: 0.3725 (tpt) REVERT: D 686 MET cc_start: 0.8606 (mmt) cc_final: 0.8323 (mmt) REVERT: D 743 MET cc_start: 0.7328 (mmp) cc_final: 0.7041 (mmm) REVERT: D 784 LEU cc_start: 0.8988 (mm) cc_final: 0.8579 (pp) REVERT: D 804 MET cc_start: 0.8558 (mmp) cc_final: 0.8209 (mmp) REVERT: D 848 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.5571 (p90) REVERT: D 854 MET cc_start: 0.8826 (mmp) cc_final: 0.8401 (tpp) REVERT: D 1116 MET cc_start: 0.7001 (mpp) cc_final: 0.6002 (ptt) REVERT: D 1122 ASP cc_start: 0.8664 (m-30) cc_final: 0.8408 (p0) REVERT: D 1143 MET cc_start: 0.2291 (mmp) cc_final: 0.0667 (mmm) REVERT: D 1166 MET cc_start: 0.6433 (tmm) cc_final: 0.5502 (ppp) outliers start: 90 outliers final: 71 residues processed: 325 average time/residue: 0.1580 time to fit residues: 84.4542 Evaluate side-chains 324 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 249 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1075 GLN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 436 HIS Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 316 ARG Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 229 optimal weight: 30.0000 chunk 261 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 875 HIS D 74 GLN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 ASN D 653 ASN ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.063773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.051080 restraints weight = 228383.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.052392 restraints weight = 148854.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.053272 restraints weight = 108565.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.053993 restraints weight = 86116.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.054463 restraints weight = 71791.433| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 27755 Z= 0.215 Angle : 0.765 14.240 37654 Z= 0.391 Chirality : 0.046 0.172 4163 Planarity : 0.006 0.076 4950 Dihedral : 7.870 88.747 3975 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 3.35 % Allowed : 19.76 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.14), residues: 3483 helix: 0.04 (0.13), residues: 1475 sheet: -0.94 (0.23), residues: 490 loop : -1.83 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 732 TYR 0.028 0.002 TYR D 503 PHE 0.032 0.003 PHE C 471 TRP 0.024 0.002 TRP D 838 HIS 0.018 0.002 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.00469 (27745) covalent geometry : angle 0.76472 (37646) SS BOND : bond 0.00325 ( 4) SS BOND : angle 1.83252 ( 8) hydrogen bonds : bond 0.04090 ( 1095) hydrogen bonds : angle 5.69643 ( 3210) Misc. bond : bond 0.00132 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 258 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9153 (tp) cc_final: 0.8928 (pt) REVERT: A 566 MET cc_start: 0.6831 (ttp) cc_final: 0.6049 (ttp) REVERT: A 583 ARG cc_start: 0.8824 (ttt180) cc_final: 0.7819 (ttt180) REVERT: A 636 ASN cc_start: 0.7609 (t0) cc_final: 0.6949 (p0) REVERT: A 641 MET cc_start: 0.5554 (ppp) cc_final: 0.5217 (ppp) REVERT: A 854 MET cc_start: 0.7114 (ppp) cc_final: 0.6872 (ppp) REVERT: A 986 ASP cc_start: 0.8512 (t0) cc_final: 0.8170 (t0) REVERT: A 1075 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: B 496 ARG cc_start: 0.8625 (mtt180) cc_final: 0.8280 (mmm160) REVERT: B 604 MET cc_start: 0.7638 (tpt) cc_final: 0.7099 (tpt) REVERT: B 754 MET cc_start: 0.9368 (mmm) cc_final: 0.9050 (mmm) REVERT: C 70 GLN cc_start: 0.8294 (pm20) cc_final: 0.8074 (pm20) REVERT: C 300 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7079 (pptt) REVERT: C 464 ASN cc_start: 0.9381 (t0) cc_final: 0.9116 (t0) REVERT: C 491 ARG cc_start: 0.9236 (ppt170) cc_final: 0.8831 (ptm-80) REVERT: C 724 MET cc_start: 0.9136 (mmm) cc_final: 0.8759 (mmm) REVERT: C 828 MET cc_start: 0.9020 (ppp) cc_final: 0.8757 (ppp) REVERT: C 1048 PHE cc_start: 0.9222 (p90) cc_final: 0.8874 (p90) REVERT: C 1077 PHE cc_start: 0.8832 (m-10) cc_final: 0.8550 (m-10) REVERT: D 74 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8533 (tp-100) REVERT: D 326 ASN cc_start: 0.8318 (m-40) cc_final: 0.7276 (t0) REVERT: D 374 ILE cc_start: 0.8872 (mm) cc_final: 0.8570 (tp) REVERT: D 604 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: D 641 MET cc_start: 0.6842 (ptm) cc_final: 0.5728 (ppp) REVERT: D 671 MET cc_start: 0.5125 (tpt) cc_final: 0.4878 (tpt) REVERT: D 686 MET cc_start: 0.8530 (mmt) cc_final: 0.8190 (mmt) REVERT: D 743 MET cc_start: 0.7308 (mmp) cc_final: 0.6958 (mmm) REVERT: D 784 LEU cc_start: 0.9074 (mm) cc_final: 0.8631 (pp) REVERT: D 804 MET cc_start: 0.8654 (mmp) cc_final: 0.8148 (mmp) REVERT: D 820 THR cc_start: 0.6522 (m) cc_final: 0.6278 (t) REVERT: D 848 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.5762 (p90) REVERT: D 1116 MET cc_start: 0.7229 (mpp) cc_final: 0.6226 (ptt) REVERT: D 1122 ASP cc_start: 0.8642 (m-30) cc_final: 0.8397 (p0) REVERT: D 1143 MET cc_start: 0.2925 (mmp) cc_final: 0.1133 (mmm) outliers start: 96 outliers final: 73 residues processed: 326 average time/residue: 0.1579 time to fit residues: 85.1282 Evaluate side-chains 321 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 244 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 816 CYS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1075 GLN Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1044 ILE Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 97 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 297 optimal weight: 9.9990 chunk 324 optimal weight: 9.9990 chunk 223 optimal weight: 0.0040 chunk 75 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 overall best weight: 3.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 879 HIS ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.064537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.051701 restraints weight = 224101.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.053010 restraints weight = 145014.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.053982 restraints weight = 105267.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.054637 restraints weight = 83155.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.055143 restraints weight = 69504.247| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 27755 Z= 0.160 Angle : 0.723 13.926 37654 Z= 0.362 Chirality : 0.045 0.193 4163 Planarity : 0.005 0.071 4950 Dihedral : 7.684 86.777 3975 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.44 % Favored : 92.54 % Rotamer: Outliers : 2.89 % Allowed : 20.32 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.14), residues: 3483 helix: 0.23 (0.13), residues: 1472 sheet: -0.97 (0.23), residues: 492 loop : -1.81 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 385 TYR 0.024 0.002 TYR C 422 PHE 0.030 0.002 PHE A 963 TRP 0.015 0.001 TRP A 607 HIS 0.011 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00360 (27745) covalent geometry : angle 0.72217 (37646) SS BOND : bond 0.00541 ( 4) SS BOND : angle 1.74529 ( 8) hydrogen bonds : bond 0.03675 ( 1095) hydrogen bonds : angle 5.50888 ( 3210) Misc. bond : bond 0.00086 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 253 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9175 (tp) cc_final: 0.8945 (pt) REVERT: A 566 MET cc_start: 0.6671 (ttp) cc_final: 0.4647 (ttp) REVERT: A 583 ARG cc_start: 0.8767 (ttt180) cc_final: 0.7811 (ttt180) REVERT: A 636 ASN cc_start: 0.7393 (t0) cc_final: 0.6718 (p0) REVERT: A 641 MET cc_start: 0.5424 (ppp) cc_final: 0.4551 (ppp) REVERT: A 675 ARG cc_start: 0.7990 (ttm170) cc_final: 0.7031 (mtm180) REVERT: A 986 ASP cc_start: 0.8563 (t0) cc_final: 0.8225 (t0) REVERT: A 1043 LYS cc_start: 0.8967 (pttm) cc_final: 0.8611 (pptt) REVERT: A 1075 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8465 (tm-30) REVERT: B 496 ARG cc_start: 0.8512 (mtt180) cc_final: 0.8130 (mmm160) REVERT: B 604 MET cc_start: 0.7574 (tpt) cc_final: 0.7057 (tpt) REVERT: B 754 MET cc_start: 0.9365 (mmm) cc_final: 0.9033 (mmm) REVERT: C 300 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7129 (pptt) REVERT: C 464 ASN cc_start: 0.9343 (t0) cc_final: 0.9041 (t0) REVERT: C 491 ARG cc_start: 0.9257 (ppt170) cc_final: 0.8335 (ptm-80) REVERT: C 604 MET cc_start: 0.8471 (tpp) cc_final: 0.7309 (tpp) REVERT: C 724 MET cc_start: 0.9153 (mmm) cc_final: 0.8737 (mmm) REVERT: C 828 MET cc_start: 0.8931 (ppp) cc_final: 0.8646 (ppp) REVERT: C 1022 ASP cc_start: 0.7860 (m-30) cc_final: 0.6951 (p0) REVERT: C 1048 PHE cc_start: 0.9128 (p90) cc_final: 0.8746 (p90) REVERT: C 1077 PHE cc_start: 0.8833 (m-10) cc_final: 0.8536 (m-10) REVERT: D 38 LYS cc_start: 0.8333 (pttm) cc_final: 0.8076 (pttm) REVERT: D 74 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8371 (mp10) REVERT: D 261 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.6008 (m-10) REVERT: D 326 ASN cc_start: 0.8328 (m-40) cc_final: 0.7363 (t0) REVERT: D 374 ILE cc_start: 0.8877 (mm) cc_final: 0.8577 (tp) REVERT: D 375 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: D 500 LEU cc_start: 0.9378 (mt) cc_final: 0.9086 (mm) REVERT: D 604 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8238 (mmm) REVERT: D 641 MET cc_start: 0.6756 (ptm) cc_final: 0.5652 (ppp) REVERT: D 671 MET cc_start: 0.5395 (tpt) cc_final: 0.5188 (tpt) REVERT: D 686 MET cc_start: 0.8569 (mmt) cc_final: 0.8137 (mmt) REVERT: D 743 MET cc_start: 0.7270 (mmp) cc_final: 0.6939 (mmm) REVERT: D 784 LEU cc_start: 0.9064 (mm) cc_final: 0.8567 (pp) REVERT: D 804 MET cc_start: 0.8580 (mmp) cc_final: 0.8137 (mmp) REVERT: D 848 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.5370 (p90) REVERT: D 920 PHE cc_start: 0.8408 (t80) cc_final: 0.8194 (t80) REVERT: D 1116 MET cc_start: 0.6973 (mpp) cc_final: 0.5903 (ptt) REVERT: D 1143 MET cc_start: 0.2823 (mmp) cc_final: 0.1022 (mmm) outliers start: 83 outliers final: 69 residues processed: 311 average time/residue: 0.1493 time to fit residues: 77.6126 Evaluate side-chains 321 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 246 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 816 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1075 GLN Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 436 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1044 ILE Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 143 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 284 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 183 optimal weight: 0.1980 chunk 194 optimal weight: 0.0670 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 overall best weight: 1.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 HIS ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.065997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.052813 restraints weight = 220201.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.054158 restraints weight = 142379.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.055212 restraints weight = 104139.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.055949 restraints weight = 81334.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.056434 restraints weight = 67163.524| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.160 27755 Z= 0.126 Angle : 0.710 13.430 37654 Z= 0.349 Chirality : 0.045 0.173 4163 Planarity : 0.005 0.064 4950 Dihedral : 7.445 87.453 3975 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.26 % Favored : 92.71 % Rotamer: Outliers : 2.41 % Allowed : 21.09 % Favored : 76.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3483 helix: 0.43 (0.14), residues: 1470 sheet: -0.81 (0.24), residues: 483 loop : -1.73 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 385 TYR 0.020 0.001 TYR C 422 PHE 0.027 0.002 PHE D 53 TRP 0.014 0.001 TRP A 624 HIS 0.011 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00293 (27745) covalent geometry : angle 0.70988 (37646) SS BOND : bond 0.00430 ( 4) SS BOND : angle 1.73309 ( 8) hydrogen bonds : bond 0.03413 ( 1095) hydrogen bonds : angle 5.32264 ( 3210) Misc. bond : bond 0.00094 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 259 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9226 (tp) cc_final: 0.8981 (pt) REVERT: A 566 MET cc_start: 0.6414 (ttp) cc_final: 0.5773 (ttp) REVERT: A 583 ARG cc_start: 0.8659 (ttt180) cc_final: 0.7675 (ttt180) REVERT: A 636 ASN cc_start: 0.7290 (t0) cc_final: 0.6619 (p0) REVERT: A 641 MET cc_start: 0.5342 (ppp) cc_final: 0.5041 (ppp) REVERT: A 986 ASP cc_start: 0.8682 (t0) cc_final: 0.8356 (t0) REVERT: A 1012 MET cc_start: 0.8151 (ppp) cc_final: 0.7171 (mmt) REVERT: A 1075 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8562 (tm130) REVERT: B 496 ARG cc_start: 0.8392 (mtt180) cc_final: 0.8049 (mmm160) REVERT: B 604 MET cc_start: 0.7318 (tpt) cc_final: 0.6800 (tpt) REVERT: B 754 MET cc_start: 0.9363 (mmm) cc_final: 0.9033 (mmm) REVERT: C 300 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7134 (pptt) REVERT: C 409 ASN cc_start: 0.7898 (t0) cc_final: 0.7593 (t0) REVERT: C 464 ASN cc_start: 0.9284 (t0) cc_final: 0.9026 (t0) REVERT: C 491 ARG cc_start: 0.9267 (ppt170) cc_final: 0.8427 (ptm-80) REVERT: C 604 MET cc_start: 0.8221 (tpp) cc_final: 0.7076 (tpp) REVERT: C 724 MET cc_start: 0.9122 (mmm) cc_final: 0.8690 (mmm) REVERT: C 828 MET cc_start: 0.8912 (ppp) cc_final: 0.8661 (ppp) REVERT: C 1048 PHE cc_start: 0.9065 (p90) cc_final: 0.8741 (p90) REVERT: C 1077 PHE cc_start: 0.8814 (m-10) cc_final: 0.8523 (m-10) REVERT: D 38 LYS cc_start: 0.8348 (pttm) cc_final: 0.8089 (pttm) REVERT: D 261 TYR cc_start: 0.6325 (OUTLIER) cc_final: 0.5914 (m-10) REVERT: D 326 ASN cc_start: 0.8287 (m-40) cc_final: 0.7321 (t0) REVERT: D 374 ILE cc_start: 0.8902 (mm) cc_final: 0.8599 (tp) REVERT: D 500 LEU cc_start: 0.9389 (mt) cc_final: 0.9098 (mm) REVERT: D 508 MET cc_start: 0.9083 (ptp) cc_final: 0.8809 (ptp) REVERT: D 604 MET cc_start: 0.8680 (ttm) cc_final: 0.8345 (tpt) REVERT: D 641 MET cc_start: 0.6801 (ptm) cc_final: 0.5847 (ppp) REVERT: D 686 MET cc_start: 0.8517 (mmt) cc_final: 0.8047 (mmt) REVERT: D 743 MET cc_start: 0.7367 (mmp) cc_final: 0.7070 (mmm) REVERT: D 804 MET cc_start: 0.8542 (mmp) cc_final: 0.8156 (mmp) REVERT: D 848 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.5341 (p90) REVERT: D 900 MET cc_start: 0.6392 (mmp) cc_final: 0.6188 (tmm) REVERT: D 920 PHE cc_start: 0.8384 (t80) cc_final: 0.8142 (t80) REVERT: D 1081 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.7293 (m-40) REVERT: D 1143 MET cc_start: 0.2875 (mmp) cc_final: 0.0799 (mmm) REVERT: D 1166 MET cc_start: 0.4978 (ppp) cc_final: 0.3943 (ppp) outliers start: 69 outliers final: 58 residues processed: 310 average time/residue: 0.1528 time to fit residues: 78.4148 Evaluate side-chains 315 residues out of total 2869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 252 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 816 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1075 GLN Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 436 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1081 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 252 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 150 optimal weight: 0.1980 chunk 271 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 253 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 chunk 191 optimal weight: 0.0570 chunk 244 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.066203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.053013 restraints weight = 217090.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.054408 restraints weight = 140188.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.055430 restraints weight = 101474.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.056117 restraints weight = 79916.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.056668 restraints weight = 66566.830| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.145 27755 Z= 0.122 Angle : 0.705 13.033 37654 Z= 0.346 Chirality : 0.045 0.188 4163 Planarity : 0.005 0.060 4950 Dihedral : 7.320 88.333 3975 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.98 % Favored : 92.99 % Rotamer: Outliers : 2.27 % Allowed : 21.37 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3483 helix: 0.46 (0.14), residues: 1474 sheet: -0.77 (0.24), residues: 476 loop : -1.72 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 385 TYR 0.018 0.001 TYR C 118 PHE 0.038 0.002 PHE D 53 TRP 0.013 0.001 TRP A 624 HIS 0.009 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00282 (27745) covalent geometry : angle 0.70462 (37646) SS BOND : bond 0.00364 ( 4) SS BOND : angle 1.76799 ( 8) hydrogen bonds : bond 0.03303 ( 1095) hydrogen bonds : angle 5.27400 ( 3210) Misc. bond : bond 0.00139 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5177.32 seconds wall clock time: 90 minutes 5.70 seconds (5405.70 seconds total)